DynDom - Protein Domain Motions

Rna-Directed RNA Polymerase

(All numbering and residues are taken from first PDB file)

Run Details Domains Sequence Morph Domain Pairs Contact Graph

DynDom run details

Property	Value
Name	Rna-Directed RNA Polymerase
Conformer 1 (PDB)	2xxd (A)
Conformer 2 (PDB)	4e76 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	306	0.84	3 - 19 37 - 145 154 - 190 201 - 202 206 - 213 216 - 216 218 - 313 315 - 315 318 - 320 325 - 350 363 - 367 397 - 397
2	227	1.87	20 - 36 146 - 153 191 - 200 203 - 205 214 - 215 217 - 217 314 - 314 316 - 317 321 - 324 351 - 362 368 - 396 398 - 543

Sequence

`_______________16__________________36___________________________________________________________________________________` `2xxd(A) : SMSYSWTGALITPCSPEEEKLPINPLSNSLLRYHNKVYCTTSKSASQRAKKVTFDRTQVLDAHYDSVLKDIKLAASKVSARLLTLEEACQLTPPHSARSKYGFGAKEVRSLSGRAVNHI` `:` `4e76(A) : SSMSYSWTGALITPCSPEEEKLPINPLSNSLLRYHNKVYCTTSKSASQRAKKVTFDRTQVLDAHYDSVLKDIKLAASKVSARLLTLQQACQLTPPHSARSKYGFGAKEVRSLSGRAVNHI` `_______________16__________________36___________________________________________________________________________________` `_______________________145_____153__________________________________190_______200__205_____213__________________________` `2xxd(A) : KSVWKDLLEDPQTPIPTTIMAKNEVFCVDPAKGGKKPARLIVYPDLGVRVCEKMALYDITQKLPQAVMGASYGFQYSPAQRVEYLLKAWAEKKDPMGFSYDTRCFDSTVTERDIRTEESI` `:` `4e76(A) : KSVWKDLLEDPQTPIPTTIMAKNEVFCVDPAKGGKKPARLIVYPDLGVRVCEKMALYDITQKLPQAVMGASYGFQYSPAQRVEYLLKAWAEKKDPMGFSYDTRCFDSTVTERDIRTEESI` `_______________________145_____153__________________________________190_______200__205_____213__________________________` `_______________________________________________________________________313____320_324_______________________350_________` `2xxd(A) : YQACSLPEEARTAIHSLTERLYVGGPMFNSKGQTCGYRRCRASGVLTTSMGNTITCYVKALAACKAAGIVAPTMLVCGDDLVVISESQGTEEDERNLRAFTEAMTRYSAPPGDPPRPEYD` `:` `4e76(A) : YQACSLPEEARTAIHSLTERLYVGGPMFNSKGQTCGYRRCRASGVLTTSMGNTITCYVKALAACKAAGIVAPTMLVCGDDLVVISESQGTEEDERNLRAFTEAMTRYSAPPGDPPRPEYD` `_______________________________________________________________________313____320_324_______________________350_________` `362_366___________________________396___________________________________________________________________________________` `2xxd(A) : LELITSCSSNVSVALGPRGRRRYYLTRDPTTPLARAAWETVRHSPINSWLGNIIQYAPTIWVRMVLMTHFFSILMVQDTLDQNLNFEMYGSVYSVNPLDLPAIIERLHGLDAFSMHTYSH` `:` `4e76(A) : LELITSCSSNVSVALGPRGRRRYYLTRDPTTPLARAAWETVRHSPINSWLGNIIQYAPTIWVRMVLMTHFFSILMVQDTLDQNLG--------GVNPLDLPAIIERLHGLDAFSMHTYSH` `362_366___________________________396___________________________________________________________________________________` `____________________________________________________________________________________` `2xxd(A) : HELTRVASALRKLGAPPLRVWKSRARAVRASLISRGGKAAVCGRYLFNWAVKTKLKLTPLPEARLLDLSSWFTVGAGGGDIFHS` `:` `4e76(A) : HELTRVASALRKLGAPPLRVWKSRARAVRASLISRGGKAAVCGRYLFNWAVKTKLKLTPLPEARLLDLSSWF***********` `____________________________________________________________________________________`

Morph

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Status: Initialising

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	11.0
Translation (A)	0.0
Closure (%)	98.2
Bending Residues ( green )	16 - 25 36 - 37 145 - 146 153 - 154 190 - 191 200 - 203 205 - 206 213 - 218 313 - 318 320 - 321 324 - 325 350 - 351 362 - 363 366 - 368 396 - 407
Bending Region Analysis

Dynamic Contact Graph

The dynamic contact graph is still being generated. Progress: Initialising

PyMOL Script

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